multiqc.nf

process MULTIQC {
    label 'process_medium'
    conda "bioconda::multiqc=1.25.1"
    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
        ? 'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0'
        : 'biocontainers/multiqc:1.25.1--pyhdfd78af_0'}"

    input:
    path workflow_summary
    path multiqc_config
    path mqc_custom_config
    path logo

    path "fastqc/*"
    path "trimgalore/fastqc/*"
    path "trimgalore/*"

    path "alignment/library/*"
    path "alignment/library/*"
    path "alignment/library/*"

    path "alignment/merged_library/unfiltered/*"
    path "alignment/merged_library/unfiltered/*"
    path "alignment/merged_library/unfiltered/*"
    path "alignment/merged_library/unfiltered/picard_metrics/*"

    path "alignment/merged_library/filtered/*"
    path "alignment/merged_library/filtered/*"
    path "alignment/merged_library/filtered/*"
    path "alignment/merged_library/filtered/picard_metrics/*"

    path "preseq/*"

    path "deeptools/*"
    path "deeptools/*"

    path "phantompeakqualtools/*"
    path "phantompeakqualtools/*"
    path "phantompeakqualtools/*"
    path "phantompeakqualtools/*"

    path "macs3/peaks/*"
    path "macs3/peaks/*"
    path "macs3/annotation/*"
    path "macs3/featurecounts/*"

    path "deseq2/*"
    path "deseq2/*"

    output:
    path "*multiqc_report.html", emit: report
    path "*_data"              , emit: data
    path "*_plots"             , optional: true, emit: plots
    path "versions.yml"        , emit: versions

    when:
    task.ext.when == null || task.ext.when

    script:
    def args          = task.ext.args ?: ''
    def custom_config = params.multiqc_config ? "--config ${mqc_custom_config}" : ''
    """
    multiqc \\
        -f \\
        ${args} \\
        ${custom_config} \\
        .

    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
    END_VERSIONS
    """
}